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Fix #1018 #1037

Merged
merged 1 commit into from
May 31, 2023
Merged

Fix #1018 #1037

merged 1 commit into from
May 31, 2023

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drpatelh
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Closes #1018

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github-actions bot commented May 31, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5dececa

+| ✅ 150 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-31 14:24:54

@drpatelh drpatelh merged commit cd0a95b into nf-core:dev May 31, 2023
MatthiasZepper
MatthiasZepper reviewed Jun 1, 2023
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I think two of the if clauses should be rephrased slightly with AND conjunctions. !skip_peudoalignment seems a bit too lenient to me.

workflows/rnaseq.nf
if (params.pseudo_aligner) { prepareToolIndices << params.pseudo_aligner }
if (!params.skip_bbsplit) { prepareToolIndices << 'bbsplit' }
if (!params.skip_alignment) { prepareToolIndices << params.aligner }
if (!params.skip_pseudo_alignment) { prepareToolIndices << params.pseudo_aligner }
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I think you should have put params.pseudo_aligner && !params.skip_pseudo_alignment here, because params.pseudo_aligner is null by default?

So it will add null to prepareToolIndices most of the time. This may or may not cause issues, depending on how prepareToolIndices is used later, but I think it preferable to avoid that in the first place?

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We are also doing parameter validation for --pseudo_aligner and --aligner via the Nextflow schema which should fail sooner before hitting this logic which is why I hadn't included it. But we can be explicit 👍🏽

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Done 993fff6

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We are also doing parameter validation for --pseudo_aligner and --aligner via the Nextflow schema which should fail sooner before hitting this logic which is why I hadn't included it. But we can be explicit 👍🏽

Admittedly, those peculiarities escaped me. I just assumed that !params.skip_pseudo_alignment will also evaluate to true when no pseudoalignment is performed at all (because the user performs a regular run with alignment).

lib/WorkflowRnaseq.groovy Show resolved Hide resolved
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@MatthiasZepper MatthiasZepper MatthiasZepper left review comments

@maxulysse maxulysse maxulysse approved these changes

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@drpatelh @maxulysse @MatthiasZepper